Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Assisted large fragment insertion by Red/ET-recombination (ALFIRE)--an alternative and enhanced method for large fragment recombineering.
PMID 17517785 · PMC1904275 · Nucleic acids research · 2007 · 6 claims · 7 setups
ALFIRE allows insertion of any fragment into small or large episomes without requiring an antibiotic selection gene in the final construct
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An "omics" approach to uropathogenic Escherichia coli vaccinology.
PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups
An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates
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C-terminal mutants of apolipoprotein L-I efficiently kill both Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense.
PMID 19997494 · PMC2778949 · PLoS pathogens · 2009 · 8 claims · 8 setups
The C-terminal helix of apoL1 is entirely responsible for its interaction with SRA
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Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.
PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups
Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).
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Strategies for folding of affinity tagged proteins using GroEL and osmolytes.
PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups
GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.
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Rats go genomic.
PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups
A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs
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Engineered apoptotic nucleases for chromatin research.
PMID 17626049 · PMC1935020 · Nucleic acids research · 2007 · 8 claims · 6 setups
Inserting TEVP cleavage sites immediately downstream of the two caspase-3 sites in DFF45 (I1I2 mutant) makes DFF40 nuclease activity exclusively dependent on TEVP cleavage (DFF-T)
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IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.
PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups
IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition
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Digital evolution.
PMID 14551915 · PMC212697 · PLoS biology · 2003 · 7 claims · 5 setups
Digital organisms (Avidians) evolved from simple self-replicators, through an unexpected transitional form, to complex performers of many logic functions, with the full genealogy traceable and no missing links.
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Systems biology and the host response to viral infection.
PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups
Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets
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Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.
PMID 17284462 · PMC1865043 · Nucleic acids research · 2007 · 6 claims · 6 setups
Cryptic lox P sites occur frequently and are homogeneously distributed across the mouse genome (1.2 primary sites per megabase).
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ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.
PMID 19097863 · PMC2723803 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups
Spontaneous KSG-resistant N. gonorrhoeae mutants arise exclusively through mutations in ksgA, not rpsI
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Alkyltransferase-mediated toxicity of 1,3-butadiene diepoxide.
PMID 18712882 · PMC2614079 · Chemical research in toxicology · 2008 · 8 claims · 6 setups
hAGT expression increases mutations and cytotoxicity following BDO exposure, and hAGT-DNA cross-links form in the presence of BDO
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Has reproduction · 67
The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.
PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups
A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.
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Has reproduction · 68
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.
PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups
A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.